Mr. Aaron Carass Profile

Aaron Carass

Research Scientist at Johns Hopkins Univ

SPIE Involvement:

Conference Program Committee | Author

Publications (79)

SPIE Journal Paper | 6 November 2024

Vector field attention for deformable image registration

Yihao Liu, Junyu Chen, Lianrui Zuo, Aaron Carass, Jerry L. Prince

JMI, Vol. 11, Issue 06, 064001, (November 2024) https://doi.org/10.1117/12.10.1117/1.JMI.11.6.064001

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Proceedings Article | 2 April 2024 Presentation + Paper

Revisiting registration-based image synthesis: a focus on unsupervised MR image synthesis

Savannah Hays, Lianrui Zuo, Yihao Liu, Anqi Feng, Jiachen Zhuo, Jerry Prince, Aaron Carass

Proceedings Volume 12926, 1292612 (2024) https://doi.org/10.1117/12.3006425

KEYWORDS: Education and training, Image segmentation, Magnetic resonance imaging, Deformation, Anatomy, Image registration, Image visualization, Image fusion, Visualization, Image processing

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Proceedings Article | 2 April 2024 Presentation + Paper

Is registering raw tagged-MR enough for strain estimation in the era of deep learning? (Image Processing Best Student Paper Award)

Zhangxing Bian, Ahmed Alshareef, Shuwen Wei, Junyu Chen, Yuli Wang, Jonghye Woo, Dzung Pham, Jiachen Zhuo, Aaron Carass, Jerry Prince

Proceedings Volume 12926, 129260A (2024) https://doi.org/10.1117/12.3006906

KEYWORDS: Deformation, Anatomy, Magnetic resonance imaging, Deep learning, Motion estimation, Motion measurement, Image registration

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Proceedings Article | 2 April 2024 Poster + Paper

Deep-learning-based segmentation of hydrocephalus brain ventricle from ultrasound

Yuli Wang, Yihao Liu, Shuwen Wei, Yuan Xue, Lianrui Zuo, Samuel Remedios, Zhangxing Bian, Michael Meggyesy, Jheesoo Ahn, Ryan Lee, Mark Luciano, Jerry Prince, Aaron Carass

Proceedings Volume 12926, 1292639 (2024) https://doi.org/10.1117/12.3007668

KEYWORDS: Ultrasonography, Image segmentation, Brain, Neuroimaging, Deep learning, Video, Magnetic resonance imaging, Education and training, Computed tomography, Convolution

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Proceedings Article | 2 April 2024 Presentation + Paper

Pushing the limits of zero-shot self-supervised super-resolution of anisotropic MR images

Samuel Remedios, Shuwen Wei, Blake Dewey, Aaron Carass, Dzung Pham, Jerry Prince

Proceedings Volume 12926, 1292606 (2024) https://doi.org/10.1117/12.3007304

KEYWORDS: Magnetic resonance imaging, Super resolution, Machine learning, Interpolation, Wavelets, Image resolution, Deep learning

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Proceedings Article | 2 April 2024 Poster + Paper

AniRes2D: anisotropic residual-enhanced diffusion for 2D MR super-resolution

Zejun Wu, Samuel Remedios, Blake Dewey, Aaron Carass, Jerry Prince

Proceedings Volume 12930, 1293029 (2024) https://doi.org/10.1117/12.3008456

KEYWORDS: Lawrencium, Magnetic resonance imaging, Super resolution, Image processing, Education and training, Diffusion, Image quality, Radon, Data modeling, Denoising

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Proceedings Article | 2 April 2024 Poster + Paper

Harmonization-enriched domain adaptation with light fine-tuning for multiple sclerosis lesion segmentation

Jinwei Zhang, Lianrui Zuo, Blake Dewey, Samuel Remedios, Savannah Hays, Dzung Pham, Jerry Prince, Aaron Carass

Proceedings Volume 12930, 129302I (2024) https://doi.org/10.1117/12.3011291

KEYWORDS: Education and training, Multiple sclerosis, Magnetic resonance imaging, Image segmentation, Solids, Fourier transforms, Scanners, White matter, Regenerative medicine, Neuroscience

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Proceedings Article | 2 April 2024 Poster + Paper

Exploratory magnetic resonance elastography synthesis from magnetic resonance and diffusion tensor imaging

Junyi Liu, Rendong Zhang, Aaron Carass, Curtis Johnson, Jerry Prince, Ahmed Alshareef

Proceedings Volume 12930, 1293028 (2024) https://doi.org/10.1117/12.3008361

KEYWORDS: Magnetic resonance elastography, Magnetic resonance imaging, Brain, Diffusion tensor imaging, Materials properties, Neuroimaging, Diffusion magnetic resonance imaging

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SPIE Journal Paper | 8 November 2023

Reproducibility evaluation of the effects of MRI defacing on brain segmentation

Chenyu Gao, Bennett Landman, Jerry Prince, Aaron Carass

JMI, Vol. 10, Issue 06, 064001, (November 2023) https://doi.org/10.1117/12.10.1117/1.JMI.10.6.064001

KEYWORDS: Image segmentation, Magnetic resonance imaging, Brain, Neuroimaging, Reproducibility, Detection and tracking algorithms, Image registration, Image processing, Image quality, Rain

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Proceedings Article | 10 April 2023 Presentation + Paper

Investigating the effect of cerebral atrophy on brain deformation using subject-specific models

Allen Hong, Aaron Carass, Lianrui Zuo, Jerry Prince, Ahmed Alshareef

Proceedings Volume 12468, 1246815 (2023) https://doi.org/10.1117/12.2654461

KEYWORDS: Brain, 3D modeling, Deformation, Traumatic brain injury, Biomechanics, Magnetic resonance imaging

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Proceedings Article | 3 April 2023 Presentation + Paper

A latent space for unsupervised MR image quality control via artifact assessment

Lianrui Zuo, Yuan Xue, Blake Dewey, Yihao Liu, Jerry Prince, Aaron Carass

Proceedings Volume 12464, 1246418 (2023) https://doi.org/10.1117/12.2652917

KEYWORDS: Image quality, Magnetic resonance imaging, Education and training, Image processing, Feature extraction

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Proceedings Article | 3 April 2023 Presentation + Paper

FastCod: fast brain connectivity in diffusion imaging

Zhangxing Bian, Muhan Shao, Jiachen Zhuo, Rao Gullapalli, Aaron Carass, Jerry Prince

Proceedings Volume 12464, 124640P (2023) https://doi.org/10.1117/12.2653644

KEYWORDS: Thalamus, Brain, Neuroimaging, Diffusion, Visualization, Magnetic resonance imaging

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Proceedings Article | 3 April 2023 Presentation + Paper

DrDisco: Deep Registration for Distortion Correction of diffusion MRI with single phase-encoding

Zhangxing Bian, Muhan Shao, Aaron Carass, Jerry Prince

Proceedings Volume 12464, 124641A (2023) https://doi.org/10.1117/12.2653649

KEYWORDS: Image registration, Diffusion magnetic resonance imaging

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Proceedings Article | 3 April 2023 Poster + Paper

Investigation of probability maps in deep-learning-based brain ventricle parcellation

Yuli Wang, Anqi Feng, Yuan Xue, Muhan Shao, Ari Blitz, Mark Luciano, Aaron Carass, Jerry Prince

Proceedings Volume 12464, 124642G (2023) https://doi.org/10.1117/12.2653999

KEYWORDS: Image segmentation, Magnetic resonance imaging, Brain mapping, Brain, Binary data, Voxels, Medicine, Image processing algorithms and systems

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Proceedings Article | 3 April 2023 Poster + Paper

Joint synthesis of WMn MPRAGE and parameter maps using deep learning and an imaging equation

Pouria Tohidi, Shuo Han, Lianrui Zuo, Jiachen Zhuo, Steven Roys, Aaron Carass, Rao Gullapalli, Jerry Prince

Proceedings Volume 12464, 124642F (2023) https://doi.org/10.1117/12.2653988

KEYWORDS: Image segmentation, Magnetic resonance imaging, Voxels, Deep learning, Thalamus, White matter, Data modeling, Visualization, Realistic image synthesis

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Proceedings Article | 3 April 2023 Poster + Paper

Unsupervised quality assurance for brain MR image rigid registration using latent shape representation

Yuan Xue, Lianrui Zuo, Samuel Remedios, Blake Dewey, Peiyu Duan, Yihao Liu, Rendong Zhang, Scott Newsome, Ellen Mowry, Aaron Carass, Jerry Prince

Proceedings Volume 12464, 124641G (2023) https://doi.org/10.1117/12.2647484

KEYWORDS: Image registration, Magnetic resonance imaging, 3D modeling, Brain, Education and training, Binary data, Rigid registration, Neuroimaging, Image quality, Multiple sclerosis

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Proceedings Article | 3 April 2023 Presentation + Paper

A deep generative prior for high-resolution isotropic MR head slices

Samuel Remedios, Blake Dewey, Aaron Carass, Dzung Pham, Jerry Prince

Proceedings Volume 12464, 124640I (2023) https://doi.org/10.1117/12.2654032

KEYWORDS: Magnetic resonance imaging, Head, Data modeling, Brain, Image resolution, Deep learning, Deep convolutional neural networks

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Proceedings Article | 3 April 2023 Poster + Paper

Segmenting thalamic nuclei from manifold projections of multi-contrast MRI

Chang Yan, Muhan Shao, Zhangxing Bian, Anqi Feng, Yuan Xue, Jiachen Zhuo, Rao Gullapalli, Aaron Carass, Jerry Prince

Proceedings Volume 12464, 1246434 (2023) https://doi.org/10.1117/12.2654405

KEYWORDS: Thalamus, Magnetic resonance imaging, Diffusion tensor imaging

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Proceedings Article | 4 April 2022 Presentation + Paper

Evaluating the impact of MR image contrast on whole brain segmentation

Savannah Hays, Lianrui Zuo, Aaron Carass, Jerry Prince

Proceedings Volume 12032, 120320I (2022) https://doi.org/10.1117/12.2611503

KEYWORDS: Magnetic resonance imaging, Image segmentation, Brain, Neuroimaging, Image processing algorithms and systems, Algorithm development, Data modeling, Visualization, Manufacturing, Magnetism

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Proceedings Article | 4 April 2022 Poster + Paper

Multiple Sclerosis brain lesion segmentation with different architecture ensembles

Pouria Tohidi, Samuel Remedios, Danielle Greenman, Muhan Shao, Shuo Han, Blake Dewey, Jacob Reinhold, Yi-Yu Chou, Dzung Pham, Jerry Prince, Aaron Carass

Proceedings Volume 12036, 1203625 (2022) https://doi.org/10.1117/12.2623302

KEYWORDS: Image segmentation, Magnetic resonance imaging, Head, Brain, Skull, Network architectures, Image filtering

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Proceedings Article | 4 April 2022 Presentation + Paper

Investigating the effect of ventricle size on brain deformation using computational models

Ahmed Alshareef, Aaron Carass, Andrew Knutsen, Kshitiz Upadhyay, Matthew Peters, K. T. Ramesh, Jerry Prince

Proceedings Volume 12036, 120360U (2022) https://doi.org/10.1117/12.2612970

KEYWORDS: Brain, 3D modeling, Traumatic brain injury, Neuroimaging, Magnetic resonance imaging, Image segmentation

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Proceedings Article | 4 April 2022 Presentation + Paper

Relationship between cerebral vasculature and brain stiffness measured using MR elastography

Ahmed Alshareef, Curtis Johnson, Aaron Carass, Andrew Knutsen, Peyton Delgorio, Grace McIlvain, Alexa Diano, K. T. Ramesh, Phillip Bayly, Dzung Pham, Jerry Prince

Proceedings Volume 12036, 120360O (2022) https://doi.org/10.1117/12.2612987

KEYWORDS: Brain, Magnetic resonance elastography, Image segmentation, Image processing, Traumatic brain injury, Neuroimaging, Mechanics, Magnetic resonance imaging

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Proceedings Article | 4 April 2022 Presentation + Paper

Evaluating the impact of MR image harmonization on thalamus deep network segmentation

Muhan Shao, Lianrui Zuo, Aaron Carass, Jiachen Zhuo, Rao Gullapalli, Jerry Prince

Proceedings Volume 12032, 120320H (2022) https://doi.org/10.1117/12.2613159

KEYWORDS: Image segmentation, Thalamus, Magnetic resonance imaging, Brain, Neuroimaging, Image processing algorithms and systems, Visualization, Diffusion tensor imaging

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Medical image segmentation is one of the core tasks of medical image analysis. Automatic segmentation of brain magnetic resonance images (MRIs) can be used to visualize and track changes of the brain’s anatomical structures that may occur due to normal aging or disease. Machine learning techniques are widely used in automatic structure segmentation. However, the contrast variation between the training and testing data makes it difficult for segmentation algorithms to generate consistent results. To address this problem, an image–to– image translation technique called MR image harmonization can be used to match the contrast between different data sets. It is important for the harmonization to transform image intensity while maintaining the underlying anatomy. In this paper, we present a 3D U-Net algorithm to segment the thalamus from multiple MR image modalities and investigate the impact of harmonization on the segmentation algorithm. Manual delineations of thalamic nuclei on two data sets are available. However, we aim to analyze the thalamus in another large data set where ground truth labels are lacking. We trained two segmentation networks, one with unharmonized images and the other with harmonized images, on one data set with manual labels, and compared their performances on the other data set with manual labels. These two data groups were diagnosed with two brain disorders and were acquired with similar imaging protocols. The harmonization target is the large data set without manual labels, which also has a different imaging protocol. The networks trained on unharmonized and harmonized data showed no significant difference when evaluating on the other data set; demonstrating that image harmonization can maintain the anatomy and does not affect the segmentation task. The two networks were evaluated on the harmonization target data set and the network trained on harmonized data showed significant improvement over the network trained on unharmonized data. Therefore, the network trained on harmonized data provides the potential to process large amounts of data from other sites, even in the absence of site-specific training data.

Proceedings Article | 4 April 2022 Presentation + Paper

Cranial meninges reconstruction based on convolutional networks and deformable models: applications to longitudinal study of normal aging

Peiyu Duan, Shuo Han, Lianrui Zuo, Yang An, Yihao Liu, Ahmed Alshareef, Junghoon Lee, Aaron Carass, Susan Resnick, Jerry Prince

Proceedings Volume 12032, 1203215 (2022) https://doi.org/10.1117/12.2613146

KEYWORDS: Brain, Magnetic resonance imaging, Statistical analysis, Spherical lenses, Reconstruction algorithms, Magnetism, Image segmentation, Data modeling, Convolutional neural networks, Statistical modeling

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Proceedings Article | 4 April 2022 Poster + Presentation + Paper

Effects of defacing whole head MRI on neuroanalysis

Chenyu Gao, Linghao Jin, Jerry Prince, Aaron Carass

Proceedings Volume 12032, 120323W (2022) https://doi.org/10.1117/12.2613175

KEYWORDS: Magnetic resonance imaging, Image segmentation, Brain, Detection and tracking algorithms, Neuroimaging, Reconstruction algorithms, Head, Image processing algorithms and systems, Magnetism, Image processing

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Proceedings Article | 15 February 2021 Presentation + Paper

Accurate estimation of total intracranial volume in MRI using a multi-tasked image-to-image translation network

Mallika Singh, Eleanor Pahl, Shangxian Wang, Aaron Carass, Junghoon Lee, Jerry Prince

Proceedings Volume 11596, 115960I (2021) https://doi.org/10.1117/12.2582264

KEYWORDS: Magnetic resonance imaging, Brain, Neuroimaging, Head, Computed tomography

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Proceedings Article | 15 February 2021 Poster + Presentation

Thalamus segmentation using convolutional neural networks

Shangxian Wang, Shuo Han, Aaron Carass, Jiachen Zhuo, Steven Roys, Rao Gullapalli, Li Jiang, Jerry Prince

Proceedings Volume 11596, 1159634 (2021) https://doi.org/10.1117/12.2582276

KEYWORDS: Image segmentation, Thalamus, Convolutional neural networks, Medical imaging, Visualization, Traumatic brain injury, Super resolution, Magnetism, Magnetic resonance imaging, Image processing algorithms and systems

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Proceedings Article | 15 February 2021 Presentation + Paper

Dynamic palatogram generation from Cine MRI for normalized speech assessment

Muhan Shao, Aaron Carass, Jiachen Zhuo, Xiao Liang, Dima Ghunaim, Maureen Stone, Jerry Prince

Proceedings Volume 11596, 115960T (2021) https://doi.org/10.1117/12.2581959

KEYWORDS: Magnetic resonance imaging, Image segmentation, Tongue, Teeth

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Proceedings Article | 15 February 2021 Poster + Presentation + Paper

Label super resolution for 3D magnetic resonance images using deformable U-net

Di Liu, Jiang Liu, Yihao Liu, Ran Tao, Jerry Prince, Aaron Carass

Proceedings Volume 11596, 1159628 (2021) https://doi.org/10.1117/12.2580932

KEYWORDS: Super resolution, Magnetism, Magnetic resonance imaging, Lawrencium, Image resolution, Image segmentation, Signal to noise ratio, Performance modeling, Medical imaging

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Proceedings Article | 15 February 2021 Presentation + Paper

Reconstruction and refinement of crossing muscle fibers in the human tongue

Muhan Shao, Arnold Gomez, Jiachen Zhuo, Xiao Liang, Maureen Stone, Aaron Carass, Jerry Prince

Proceedings Volume 11596, 115961K (2021) https://doi.org/10.1117/12.2582287

KEYWORDS: Tongue, Diffusion weighted imaging, Spherical lenses, High angular resolution diffusion imaging, Convolutional neural networks, Brain, Anisotropic diffusion

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Proceedings Article | 10 March 2020 Presentation + Paper

Finding novelty with uncertainty

Jacob Reinhold, Yufan He, Shizhong Han, Yunqiang Chen, Dashan Gao, Junghoon Lee, Jerry Prince, Aaron Carass

Proceedings Volume 11313, 113130H (2020) https://doi.org/10.1117/12.2549341

KEYWORDS: Image segmentation, Computed tomography, Pathology, Data modeling, Medical imaging, Brain, Magnetic resonance imaging, Neural networks, Statistical modeling, Head

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Proceedings Article | 10 March 2020 Paper

Variational intensity cross channel encoder for unsupervised vessel segmentation on OCT angiography

Yihao Liu, Lianrui Zuo, Aaron Carass, Yufan He, Angeliki Filippatou, Sharon Solomon, Shiv Saidha, Peter Calabresi, Jerry Prince

Proceedings Volume 11313, 113130Y (2020) https://doi.org/10.1117/12.2549967

KEYWORDS: Image segmentation, Angiography, Optical coherence tomography, Network architectures, Capillaries, Eye

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Proceedings Article | 10 March 2020 Paper

Segmenting retinal OCT images with inter-B-scan and longitudinal information

Yufan He, Aaron Carass, Yihao Liu, Angeliki Filippatou, Bruno Jedynak, Sharon Solomon, Shiv Saidha, Peter Calabresi, Jerry Prince

Proceedings Volume 11313, 113133C (2020) https://doi.org/10.1117/12.2549857

KEYWORDS: Image segmentation, Optical coherence tomography, 3D image processing, Convolution, Image registration, Network architectures, Retina, Computer programming

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Proceedings Article | 10 March 2020 Paper

Reflection-equivariant convolutional neural networks improve segmentation over reflection augmentation

Shuo Han, Jerry Prince, Aaron Carass

Proceedings Volume 11313, 1131337 (2020) https://doi.org/10.1117/12.2549399

KEYWORDS: Image segmentation, Brain, Convolution, Neuroimaging, Convolutional neural networks, Cerebellum, Magnetic resonance imaging, Network architectures

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Proceedings Article | 10 March 2020 Presentation + Paper

Adversarial domain adaptation for multi-device retinal OCT segmentation

Yufan He, Aaron Carass, Yihao Liu, Shiv Saidha, Peter Calabresi, Jerry Prince

Proceedings Volume 11313, 1131309 (2020) https://doi.org/10.1117/12.2549839

KEYWORDS: Image segmentation, Data modeling, Optical coherence tomography, Convolution

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Proceedings Article | 15 March 2019 Presentation + Paper

Cerebellum parcellation with convolutional neural networks

Shuo Han, Yufan He, Aaron Carass, Sarah Ying, Jerry Prince

Proceedings Volume 10949, 109490K (2019) https://doi.org/10.1117/12.2512119

KEYWORDS: Cerebellum, Image segmentation, Convolutional neural networks, Magnetic resonance imaging, Network architectures, Image processing algorithms and systems, Medicine

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Proceedings Article | 15 March 2019 Presentation + Paper

Automatic quality control using hierarchical shape analysis for cerebellum parcellation

Lianrui Zuo, Shuo Han, Aaron Carass, Sarah Ying, Chiadikaobi Onyike, Jerry Prince

Proceedings Volume 10949, 109490J (2019) https://doi.org/10.1117/12.2512805

KEYWORDS: Cerebellum, Image segmentation, Shape analysis, Automatic control, Error analysis, Medicine, Visualization, Computer engineering, Biomedical engineering, Behavioral neuroscience

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Proceedings Article | 15 March 2019 Paper

Evaluating the impact of intensity normalization on MR image synthesis

Jacob Reinhold, Blake Dewey, Aaron Carass, Jerry Prince

Proceedings Volume 10949, 109493H (2019) https://doi.org/10.1117/12.2513089

KEYWORDS: Magnetic resonance imaging, Brain, Image segmentation, Neuroimaging, Image quality, Image registration, Image restoration, Image processing, Computed tomography

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Proceedings Article | 12 March 2018 Presentation + Paper

Inverse biomechanical modeling of the tongue via machine learning and synthetic training data

Aniket Tolpadi, Maureen Stone, Aaron Carass, Jerry Prince, Arnold Gomez

Proceedings Volume 10576, 1057606 (2018) https://doi.org/10.1117/12.2296927

KEYWORDS: Data modeling, Tongue, Machine learning, Magnetic resonance imaging, Wavelets, Calibration, Motion measurement, Tissues, Motion estimation, Computer simulations

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Proceedings Article | 12 March 2018 Presentation + Paper

Improving self super resolution in magnetic resonance images

Sachin Goyal, Can Zhao, Amod Jog, Jerry Prince, Aaron Carass

Proceedings Volume 10578, 1057814 (2018) https://doi.org/10.1117/12.2295366

KEYWORDS: Image resolution, Magnetic resonance imaging, Lawrencium, Super resolution, Magnetism, Spatial resolution, Image filtering, Image analysis, Data modeling, Signal to noise ratio

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Proceedings Article | 12 March 2018 Presentation + Paper

Automatic outlier detection using hidden Markov model for cerebellar lobule segmentation

Lianrui Zuo, Aaron Carass, Shuo Han, Jerry Prince

Proceedings Volume 10578, 105780D (2018) https://doi.org/10.1117/12.2295709

KEYWORDS: Image segmentation, Cerebellum, Image classification, Error analysis, Failure analysis, Visualization, Medical imaging, Feature extraction, Probability theory, Image processing algorithms and systems

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Proceedings Article | 12 March 2018 Presentation + Paper

Multi-atlas segmentation of the hydrocephalus brain using an adaptive ventricle atlas

Muhan Shao, Aaron Carass, Xiang Li, Blake Dewey, Ari Blitz, Jerry Prince, Lotta Ellingsen

Proceedings Volume 10578, 105780F (2018) https://doi.org/10.1117/12.2295613

KEYWORDS: Brain, Image segmentation, Magnetic resonance imaging, Image registration, Diagnostics, Image fusion, Surgery, Dementia

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Proceedings Article | 2 March 2018 Paper

Deformable model reconstruction of the subarachnoid space

Jeffrey Glaister, Muhan Shao, Xiang Li, Aaron Carass, Snehashis Roy, Ari Blitz, Jerry Prince, Lotta Ellingsen

Proceedings Volume 10574, 1057431 (2018) https://doi.org/10.1117/12.2293633

KEYWORDS: Magnetic resonance imaging, Brain, Cerebellum, Image segmentation, Head, Cerebrum, Brain mapping, Computer engineering

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Proceedings Article | 2 March 2018 Presentation + Paper

Inter-scanner variation independent descriptors for constrained diffeomorphic demons registration of retina OCT

S. Reaungamornrat, A. Carass, Y. He, S. Saidha, P. Calabresi, J. Prince

Proceedings Volume 10574, 105741B (2018) https://doi.org/10.1117/12.2293790

KEYWORDS: Optical coherence tomography, Image registration, Denoising, Silver, Retina, Image quality, Image resolution, Speckle, Image segmentation, Rigid registration

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Purpose: OCT offers high in-plane micrometer resolution, enabling studies of neurodegenerative and ocular-disease mechanisms via imaging of the retina at low cost. An important component to such studies is inter-scanner deformable image registration. Image quality of OCT, however, is suboptimal with poor signal-to-noise ratio and through-plane resolution. Geometry of OCT is additionally improperly defined. We developed a diffeomorphic deformable registration method incorporating constraints accommodating the improper geometry and a decentralized-modality-insensitiveneighborhood-descriptors (D-MIND) robust against degradation of OCT image quality and inter-scanner variability. Method: The method, called D-MIND Demons, estimates diffeomorphisms using D-MINDs under constraints on the direction of velocity fields in a MIND-Demons framework. Descriptiveness of D-MINDs with/without denoising was ranked against four other shape/texture-based descriptors. Performance of D-MIND Demons and its variants incorporating other descriptors was compared for cross-scanner, intra- and inter-subject deformable registration using clinical retina OCT data. Result: D-MINDs outperformed other descriptors with the difference in mutual descriptiveness between high-contrast and homogenous regions > 0.2. Among Demons variants, D-MIND-Demons was computationally efficient, demonstrating robustness against OCT image degradation (noise, speckle, intensity-non-uniformity, and poor throughplane resolution) and consistent registration accuracy [(4±4 μm) and (4±6 μm) in cross-scanner intra- and inter-subject registration] regardless of denoising. Conclusions: A promising method for cross-scanner, intra- and inter-subject OCT image registration has been developed for ophthalmological and neurological studies of retinal structures. The approach could assist image segmentation, evaluation of longitudinal disease progression, and patient population analysis, which in turn, facilitate diagnosis and patient-specific treatment.

Proceedings Article | 13 March 2017 Paper

Collaborative SDOCT segmentation and analysis software

Yeyi Yun, Aaron Carass, Andrew Lang, Jerry Prince, Bhavna Antony

Proceedings Volume 10138, 1013813 (2017) https://doi.org/10.1117/12.2254050

KEYWORDS: Image segmentation, Human-machine interfaces, Visualization, Scanners, Analytical research, Optical coherence tomography, Databases, Visual analytics, Scanning laser ophthalmoscopy, Image analysis

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Proceedings Article | 13 March 2017 Presentation + Paper

Efficient multi-atlas registration using an intermediate template image

Blake Dewey, Aaron Carass, Ari Blitz, Jerry Prince

Proceedings Volume 10137, 101371F (2017) https://doi.org/10.1117/12.2256147

KEYWORDS: Image registration, Image fusion, Brain, Image restoration, Image processing, Neuroimaging, Image analysis, Medical imaging, Expectation maximization algorithms, Clinical research

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Proceedings Article | 13 March 2017 Presentation + Paper

Longitudinal analysis of mouse SDOCT volumes

Bhavna Antony, Aaron Carass, Andrew Lang, Byung-Jin Kim, Donald Zack, Jerry Prince

Proceedings Volume 10137, 101371H (2017) https://doi.org/10.1117/12.2257432

KEYWORDS: Optical coherence tomography, Animal model studies, Eye models, Image registration, Image segmentation, Retina, Blood vessels, Optic nerve, Head, Image processing, Control systems, Clouds

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Proceedings Article | 13 March 2017 Presentation + Paper

Automatic falx cerebri and tentorium cerebelli segmentation from magnetic resonance images

Jeffrey Glaister, Aaron Carass, Dzung Pham, John Butman, Jerry Prince

Proceedings Volume 10137, 101371D (2017) https://doi.org/10.1117/12.2255640

KEYWORDS: Image segmentation, Brain, Reconstruction algorithms, Magnetic resonance imaging, Finite element methods, Head, Image processing algorithms and systems, 3D visualizations, Image processing, Neuroimaging, Cerebrum, Cerebellum, Tissues

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Proceedings Article | 13 March 2017 Paper

Improving graph-based OCT segmentation for severe pathology in retinitis pigmentosa patients

Andrew Lang, Aaron Carass, Ava Bittner, Howard Ying, Jerry Prince

Proceedings Volume 10137, 101371M (2017) https://doi.org/10.1117/12.2254849

KEYWORDS: Error analysis, Optical coherence tomography, Algorithm development, Pathology, Retina, 3D image processing, Data analysis, Probability theory, Control systems, Data acquisition, Image processing algorithms and systems, Image segmentation

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Proceedings Article | 24 February 2017 Presentation + Paper

Multi-atlas-based CT synthesis from conventional MRI with patch-based refinement for MRI-based radiotherapy planning

Junghoon Lee, Aaron Carass, Amod Jog, Can Zhao, Jerry Prince

Proceedings Volume 10133, 101331I (2017) https://doi.org/10.1117/12.2254571

KEYWORDS: Tumors, Image fusion, X-ray computed tomography, Bone

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Proceedings Article | 29 March 2016 Paper

Voxel based morphometry in optical coherence tomography: validation and core findings

Bhavna Antony, Min Chen, Aaron Carass, Bruno Jedynak, Omar Al-Louzi, Sharon Solomon, Shiv Saidha, Peter Calabresi, Jerry Prince

Proceedings Volume 9788, 97880P (2016) https://doi.org/10.1117/12.2216096

KEYWORDS: Optical coherence tomography, Retina, Image registration, Image processing, Image segmentation, Statistical analysis, Tissues, Visualization, Medicine

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Proceedings Article | 24 March 2016 Paper

A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction

S. Mazdak Abulnaga, Zhen Yang, Aaron Carass, Kalyani Kansal, Bruno Jedynak, Chiadi Onyike, Sarah Ying, Jerry Prince

Proceedings Volume 9785, 97852P (2016) https://doi.org/10.1117/12.2216584

KEYWORDS: Computer engineering, Visualization, Visual analytics, Shape analysis, Cerebellum, Principal component analysis, MATLAB, Dimension reduction, Head, Magnetic resonance imaging, Image analysis, Neodymium

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Proceedings Article | 21 March 2016 Paper

Quality assurance using outlier detection on an automatic segmentation method for the cerebellar peduncles

Ke Li, Chuyang Ye, Zhen Yang, Aaron Carass, Sarah Ying, Jerry Prince

Proceedings Volume 9784, 97841H (2016) https://doi.org/10.1117/12.2217309

KEYWORDS: Image segmentation, Diffusion tensor imaging, Image quality, Cerebellum, Brain, Medical imaging, Control systems, Feature extraction

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Proceedings Article | 21 March 2016 Paper

Simultaneous segmentation of retinal surfaces and microcystic macular edema in SDOCT volumes

Bhavna Antony, Andrew Lang, Emily Swingle, Omar Al-Louzi, Aaron Carass, Sharon Solomon, Peter Calabresi, Shiv Saidha, Jerry Prince

Proceedings Volume 9784, 97841C (2016) https://doi.org/10.1117/12.2214676

KEYWORDS: Image segmentation, Optical coherence tomography, Algorithm development, Medical imaging, Medicine, Scanning laser ophthalmoscopes

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Proceedings Article | 21 March 2016 Paper

Combining multi-atlas segmentation with brain surface estimation

Yuankai Huo, Aaron Carass, Susan Resnick, Dzung Pham, Jerry Prince, Bennett Landman

Proceedings Volume 9784, 97840E (2016) https://doi.org/10.1117/12.2216604

KEYWORDS: Brain, Image segmentation, Neuroimaging, Magnetic resonance imaging, Cerebral cortex, Error analysis, Image fusion, Reconstruction algorithms

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Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this “segmentation to surface to parcellation” strategy has shown limitation in various situations. In this work, we propose a novel “multi-atlas segmentation to surface” method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly population.

Proceedings Article | 21 March 2016 Paper

Segmentation and labeling of the ventricular system in normal pressure hydrocephalus using patch-based tissue classification and multi-atlas labeling

Lotta Ellingsen, Snehashis Roy, Aaron Carass, Ari Blitz, Dzung Pham, Jerry Prince

Proceedings Volume 9784, 97840G (2016) https://doi.org/10.1117/12.2216511

KEYWORDS: Magnetic resonance imaging, Tissues, Dementia, Classification systems, Gait analysis, Surgery, Diagnostics, Magnetism, Image segmentation, Alzheimer's disease, Brain, Image registration

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Proceedings Article | 21 March 2016 Paper

Thalamus parcellation using multi-modal feature classification and thalamic nuclei priors

Jeffrey Glaister, Aaron Carass, Joshua Stough, Peter Calabresi, Jerry Prince

Proceedings Volume 9784, 97843J (2016) https://doi.org/10.1117/12.2216987

KEYWORDS: Thalamus, Image segmentation, Image processing algorithms and systems, Diffusion magnetic resonance imaging, Magnetic resonance imaging, Machine learning, Magnetism, Algorithm development, Diffusion, Diffusion tensor imaging, Brain, Neuroimaging, Feature extraction

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Proceedings Article | 21 March 2016 Paper

Segmentation of thalamus from MR images via task-driven dictionary learning

Luoluo Liu, Jeffrey Glaister, Xiaoxia Sun, Aaron Carass, Trac Tran, Jerry Prince

Proceedings Volume 9784, 97843H (2016) https://doi.org/10.1117/12.2214206

KEYWORDS: Thalamus, Associative arrays, Image segmentation, Magnetic resonance imaging, Diffusion tensor imaging, Stochastic processes, Feature extraction, Binary data, Automatic tracking, Chemical species

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Proceedings Article | 21 March 2016 Paper

Combined registration and motion correction of longitudinal retinal OCT data

Andrew Lang, Aaron Carass, Omar Al-Louzi, Pavan Bhargava, Sharon Solomon, Peter Calabresi, Jerry Prince

Proceedings Volume 9784, 97840X (2016) https://doi.org/10.1117/12.2217157

KEYWORDS: Image registration, Optical coherence tomography, Retina, Eye, Blood vessels, Motion estimation, Image segmentation, Image processing, Data acquisition, Scanners

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Proceedings Article | 21 March 2016 Paper

Landmark based shape analysis for cerebellar ataxia classification and cerebellar atrophy pattern visualization

Zhen Yang, S. Mazdak Abulnaga, Aaron Carass, Kalyani Kansal, Bruno Jedynak, Chiadi Onyike, Sarah Ying, Jerry Prince

Proceedings Volume 9784, 97840P (2016) https://doi.org/10.1117/12.2217313

KEYWORDS: Magnetic resonance imaging, Brain imaging, Statistical analysis, Image segmentation, Neodymium, Computer engineering

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Proceedings Article | 21 March 2016 Paper

Effects of spatial resolution on image registration

Can Zhao, Aaron Carass, Amod Jog, Jerry Prince

Proceedings Volume 9784, 97840Y (2016) https://doi.org/10.1117/12.2217322

KEYWORDS: Image registration, Spatial resolution, Image resolution, Image restoration, Statistical analysis, Lawrencium, Neuroimaging, Brain, Rutherfordium, Image fusion, Medical imaging, Digital imaging

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Proceedings Article | 20 March 2015 Paper

Longitudinal graph-based segmentation of macular OCT using fundus alignment

Andrew Lang, Aaron Carass, Omar Al-Louzi, Pavan Bhargava, Howard Ying, Peter Calabresi, Jerry Prince

Proceedings Volume 9413, 94130M (2015) https://doi.org/10.1117/12.2077713

KEYWORDS: Optical coherence tomography, Image segmentation, Lawrencium, Retina, Image registration, Algorithm development, Optical alignment, Medicine, Diagnostics, Failure analysis

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Proceedings Article | 20 March 2015 Paper

Multi-output decision trees for lesion segmentation in multiple sclerosis

Amod Jog, Aaron Carass, Dzung Pham, Jerry Prince

Proceedings Volume 9413, 94131C (2015) https://doi.org/10.1117/12.2082157

KEYWORDS: Image segmentation, Magnetic resonance imaging, Tissues, Brain, Detection and tracking algorithms, Nervous system, Image processing, Feature extraction, Neurons, Spinal cord

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Proceedings Article | 20 March 2015 Paper

Using image synthesis for multi-channel registration of different image modalities

Min Chen, Amog Jog, Aaron Carass, Jerry Prince

Proceedings Volume 9413, 94131Q (2015) https://doi.org/10.1117/12.2082373

KEYWORDS: Image registration, Detection and tracking algorithms, Magnetic resonance imaging, Image restoration, Image segmentation, Magnetism, Switching, Medical imaging, Image processing, Cerebrum

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Proceedings Article | 17 March 2015 Paper

Segmentation of microcystic macular edema in Cirrus OCT scans with an exploratory longitudinal study

Emily Swingle, Andrew Lang, Aaron Carass, Omar Al-Louzi, Shiv Saidha, Jerry Prince, Peter Calabresi

Proceedings Volume 9417, 94170P (2015) https://doi.org/10.1117/12.2082164

KEYWORDS: Optical coherence tomography, Image segmentation, Signal to noise ratio, Retina, Scanners, Image processing algorithms and systems, Digital filtering, Pathology, Image quality, Diagnostics

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Proceedings Article | 21 March 2014 Paper

MR to CT registration of brains using image synthesis

Snehashis Roy, Aaron Carass, Amod Jog, Jerry Prince, Junghoon Lee

Proceedings Volume 9034, 903419 (2014) https://doi.org/10.1117/12.2043954

KEYWORDS: Magnetic resonance imaging, Computed tomography, Image registration, Brain, Neuroimaging, Tissues, Radiotherapy, Tumors, Image segmentation, Clouds

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Proceedings Article | 21 March 2014 Paper

An adaptive grid for graph-based segmentation in retinal OCT

Andrew Lang, Aaron Carass, Peter Calabresi, Howard Ying, Jerry Prince

Proceedings Volume 9034, 903402 (2014) https://doi.org/10.1117/12.2043040

KEYWORDS: Retina, Image segmentation, Optical coherence tomography, Data modeling, Macula, Algorithm development, Image processing algorithms and systems, Medicine, Eye, Scanners

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Proceedings Article | 21 March 2014 Paper

Example based lesion segmentation

Snehashis Roy, Qing He, Aaron Carass, Amod Jog, Jennifer Cuzzocreo, Daniel Reich, Jerry Prince, Dzung Pham

Proceedings Volume 9034, 90341Y (2014) https://doi.org/10.1117/12.2043917

KEYWORDS: Image segmentation, Magnetic resonance imaging, Model-based design, Associative arrays, Alzheimer's disease, 3D modeling, Neurological disorders, Ischemia, 3D image processing, Tissues

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Proceedings Article | 13 March 2014 Paper

Microcystic macular edema detection in retina OCT images

Emily Swingle, Andrew Lang, Aaron Carass, Howard Ying, Peter Calabresi, Jerry Prince

Proceedings Volume 9038, 90380G (2014) https://doi.org/10.1117/12.2043910

KEYWORDS: Optical coherence tomography, Retina, Image segmentation, Control systems, Detection and tracking algorithms, Macula, Eye, Tissues, Neodymium, Analytical research

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Proceedings Article | 13 March 2013 Paper

Automatic cell segmentation in fluorescence images of confluent cell monolayers using multi-object geometric deformable model

Zhen Yang, John Bogovic, Aaron Carass, Mao Ye, Peter Searson, Jerry Prince

Proceedings Volume 8669, 866904 (2013) https://doi.org/10.1117/12.2006603

KEYWORDS: Image segmentation, Image enhancement, Image analysis, Chromium, Luminescence, Image processing, Image processing algorithms and systems, Microscopy, Electroluminescent displays, Computer engineering

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Proceedings Article | 13 March 2013 Paper

Pulse sequence based multi-acquisition MR intensity normalization

Amod Jog, Snehashis Roy, Aaron Carass, Jerry Prince

Proceedings Volume 8669, 86692H (2013) https://doi.org/10.1117/12.2007062

KEYWORDS: Tissues, Magnetic resonance imaging, Brain, Neuroimaging, Image analysis, Physics, Magnetism, Scanners, Biology, Evolutionary algorithms

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Proceedings Article | 13 March 2013 Paper

Segmentation of retinal OCT images using a random forest classifier

Andrew Lang, Aaron Carass, Elias Sotirchos, Peter Calabresi, Jerry Prince

Proceedings Volume 8669, 86690R (2013) https://doi.org/10.1117/12.2006649

KEYWORDS: Image segmentation, Optical coherence tomography, Retina, Blood vessels, Feature extraction, Image processing, Image processing algorithms and systems, 3D modeling, Smoothing, Software development

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Proceedings Article | 13 March 2013 Paper

Longitudinal intensity normalization of magnetic resonance images using patches

Snehashis Roy, Aaron Carass, Jerry Prince

Proceedings Volume 8669, 86691J (2013) https://doi.org/10.1117/12.2006682

KEYWORDS: Image segmentation, Tissues, Magnetism, Brain, Magnetic resonance imaging, Image processing algorithms and systems, 3D image processing, Neuroimaging, Image processing, Statistical analysis

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Proceedings Article | 13 March 2013 Paper

Voxel-wise displacement as independent features in classification of multiple sclerosis

Min Chen, Aaron Carass, Daniel Reich, Peter Calabresi, Dzung Pham, Jerry Prince

Proceedings Volume 8669, 86690K (2013) https://doi.org/10.1117/12.2007150

KEYWORDS: Electroluminescent displays, Image registration, Magnetic resonance imaging, Brain, Control systems, Neuroimaging, Scanning probe microscopy, Magnetism, Associative arrays, Image fusion

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Proceedings Article | 13 March 2013 Paper

Automated anatomical labeling of the cerebral arteries using belief propagation

Murat Bilgel, Snehashis Roy, Aaron Carass, Paul Nyquist, Jerry Prince

Proceedings Volume 8669, 866918 (2013) https://doi.org/10.1117/12.2006460

KEYWORDS: Arteries, Image segmentation, Statistical inference, Brain, Independent component analysis, Matrices, Medicine, Magnetic resonance imaging, 3D modeling, Expectation maximization algorithms

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Proceedings Article | 14 February 2012 Paper

Simultaneous cortical surface labeling and sulcal curve extraction

Zhen Yang, Aaron Carass, Chen Chen, Jerry Prince

Proceedings Volume 8314, 831414 (2012) https://doi.org/10.1117/12.910552

KEYWORDS: Expectation maximization algorithms, Optical spheres, Error analysis, Statistical modeling, Computer engineering, Data modeling, Brain, Image segmentation, Principal component analysis, Detection and tracking algorithms

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Proceedings Article | 11 March 2011 Paper

Intensity inhomogeneity correction of magnetic resonance images using patches

Snehashis Roy, Aaron Carass, Pierre-Louis Bazin, Jerry Prince

Proceedings Volume 7962, 79621F (2011) https://doi.org/10.1117/12.877466

KEYWORDS: Image segmentation, Magnetic resonance imaging, Magnetism, Image processing, Brain, Neuroimaging, Image acquisition, Distortion, Tissues, Statistical analysis

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Proceedings Article | 11 March 2011 Paper

Distance transforms in multichannel MR image registration

Min Chen, Aaron Carass, John Bogovic, Pierre-Louis Bazin, Jerry Prince

Proceedings Volume 7962, 79621D (2011) https://doi.org/10.1117/12.878367

KEYWORDS: Image segmentation, Image registration, Transform theory, Magnetic resonance imaging, Brain, Neuroimaging, Medical imaging, Image restoration, Detection and tracking algorithms, Image processing algorithms and systems

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Proceedings Article | 13 March 2010 Paper

Synthesizing MR contrast and resolution through a patch matching technique

Snehashis Roy, Aaron Carass, Jerry Prince

Proceedings Volume 7623, 76230J (2010) https://doi.org/10.1117/12.844575

KEYWORDS: Image resolution, Tissues, Magnetic resonance imaging, Neuroimaging, Image segmentation, Information visualization, Data acquisition, Image processing, Image analysis, Brain

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